Some apps are not masked for a reason I don't know. Only app store apps are masked unless it's a custom icon. Cydia apps/tweaks need a custom icon in order to be themed. Leave a request for a custom icon here

Awesome theme by the way. I like how subtle is it. It doesn't 'jump out' and scream like other themes. Just damn classy. Was on Jaku for a long while before going to EPHD2012 and then back to Jaku after the new JB was out. And it is really nice this requires 0 setup, literally. Just tick the relevant Ayecon theme on Winterboard and respring and you're good to go. Gonna stick to this for some time. Oh also, as someone has mentioned earlier, a nice retina keyboard for colour keyboard would be nice!

for some reason i cant get the phone png. to change to black any help?

Navigate to: Library/Themes/ayecon SpringBoard.theme/Bundles/com.apple.mobilephone and change
1. "[email protected]" to "icon@2x(white).png" AND "icon@2x~iphone.png" to "icon@2x~iphone(white).png"
THEN
2. "icon@2x~iphone(BLK).png" to "icon@2x~iphone.png" AND "icon@2x(BLK)" to "[email protected]"